Python Workbench

Description

This workspace types comes with various Python development tools already installed:

  • pyenv for managing different python versions
  • miniconda for managing dependency environments
  • poetry for an alternative way of running projects with specified dependencies

There are various flavours of this Catalog Item:

Simply choose the one that is most convenient to you.

Tools are installed in userspace

Note that the above tools are installed separately for each user in your CO that has access to the machine. This means each user can have their own clean pyenv and miniconda environments.

If you prefer all users on the machine to have a single shared miniconda environment, please see the Miniconda Catalog Item.

Creation

Create a storage volume

If desired, first create a storage volume before creating the workspace.

See the Getting started page for more info about how and why to create a storage volume.

Create a workspace

In the Research Cloud portal click the ‘Create a new workspace’ button and follow the steps in the wizzard.

See the workspace creation manual page for more guidance.

Access

Python Workbench CLI

For the Python Workbench CLI (command line) flavour of this Catalog Item, you can login using SSH.

Python Workbench Desktop

For the Python Workbench Desktop flavour of this Catalog Item, you can login using your browser. It is also possible to login via SSH, as described above.

Usage

The first time (but only the first time) you login to a workspace of this type, the Python tools (pyenv, miniconda and poetry) are installed for your user. This means that at first login you may experience a small delay (~1 minute maximum). During this time, if you are logging in on the command line, you will see that the applications are being installed for you:

--- Running install scripts at first login: executing /home/username/runonce.d/01_pyenv-install.sh
--- Running install scripts at first login: executing /home/username/runonce.d/10-poetry.sh
--- Running install scripts at first login: executing /home/username/runonce.d/runonce_conda.sh

When you are logged in you can start developing or running code. On the command line, you will have pyenv, miniconda, and poetry available.

By default, pyenv will be configured to use the most recent version of Python shipped with the operating system:

$ pyenv versions
  system
* system-latest (set by /home/testuser/.pyenv/version)

You can use pyenv to install and select a different (newer) Python version: e.g. pyenv install 3.12, pyenv global 3.12. See the pyenv docs.

To start using miniconda environments, activate conda with the command conda init. See the miniconda docs.

Also see the poetry docs.

Data transfer options

See our data transfer manuals.

The recommended iBridges client for Yoda and iRODS is preinstalled.

Installing additional software

The user has admin rights to install additional software on the system from the terminal.

Tips

Workspace security

Please take a moment to read the security recommendations for VREs.